LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units           lj
atom_style      atomic

pair_style      lj/cut 2.5

read_data       data.rigid
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  81 atoms
  read_data CPU = 0.000 seconds

velocity        all create 100.0 4928459

# unconnected bodies

group           clump1 id <> 1 9
9 atoms in group clump1
group           clump2 id <> 10 18
9 atoms in group clump2
group           clump3 id <> 19 27
9 atoms in group clump3
group           clump4 id <> 28 36
9 atoms in group clump4
group           clump5 id <> 37 45
9 atoms in group clump5
group           clump6 id <> 46 54
9 atoms in group clump6
group           clump7 id <> 55 63
9 atoms in group clump7
group           clump8 id <> 64 72
9 atoms in group clump8
group           clump9 id <> 73 81
9 atoms in group clump9

fix 1 all poems file unconnected-bodies.dat
WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035)
9 clusters, 9 bodies, 0 joints, 81 atoms

neigh_modify    exclude group clump1 clump1
neigh_modify    exclude group clump2 clump2
neigh_modify    exclude group clump3 clump3
neigh_modify    exclude group clump4 clump4
neigh_modify    exclude group clump5 clump5
neigh_modify    exclude group clump6 clump6
neigh_modify    exclude group clump7 clump7
neigh_modify    exclude group clump8 clump8
neigh_modify    exclude group clump9 clump9

thermo          100

#dump           1 all atom 50 dump.rigid.poems

#dump           2 all image 100 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    2 pad 5

#dump           3 all movie 100 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    3 pad 5

timestep        0.0001
thermo          50
run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix poems command:

@Article{Mukherjee08,
 author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
 title = {Substructured molecular dynamics using multibody dynamics algorithms},
 journal = {Intl.~J.~Non-linear Mechanics},
 year =    2008,
 volume =  43,
 pages =   {1045--1055}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    115.29439    5235.9179            0    5272.2142   -2.7403788 
      50    14910.686    571.71596            0    5265.8207    32.006226 
     100      16298.5    136.65142            0    5267.6607    16.443791 
     150    16682.639    17.488068            0      5269.43    14.900278 
     200    16733.955    1.3724268            0    5269.4692    14.569123 
     250    16738.877  -0.15250573            0    5269.4939    14.496287 
     300    16738.611  -0.05516662            0    5269.5077    14.495909 
     350    16738.515  -0.01744351            0    5269.5152    14.496329 
     400    16738.488 -0.0060096677            0    5269.5178    14.496497 
     450    16738.479 -0.0012712918            0    5269.5199    14.496575 
     500    16738.479 -0.00081070354            0    5269.5203     14.49658 
     550    16738.479 -0.00083205205            0    5269.5203    14.496577 
     600    16738.479 -0.0005835658            0    5269.5206     14.49658 
     650    16738.479 -0.00047227225            0    5269.5206    14.496583 
     700    16738.479            0            0     5269.521    14.496593 
     750    16738.479            0            0    5269.5211    14.496595 
     800    16738.479            0            0    5269.5211    14.496596 
     850    16738.479            0            0    5269.5211    14.496595 
     900    16738.479            0            0    5269.5212    14.496593 
     950    16738.485 -0.003532391            0    5269.5196    14.496546 
    1000    16738.609 -0.051135033            0    5269.5109    14.496098 
    1050    16737.381   0.32991002            0    5269.5055    14.525627 
    1100    16737.915   0.16210932            0    5269.5058    14.531848 
    1150    16738.726 -0.089235332            0    5269.5098    14.509768 
    1200     16738.49 -0.0075446298            0    5269.5169    14.510489 
    1250     16738.48            0            0    5269.5214    14.510585 
    1300     16738.48            0            0    5269.5214    14.510587 
    1350     16738.48            0            0    5269.5215    14.510588 
    1400     16738.48 -0.00044742303            0    5269.5211    14.510581 
    1450    16738.481 -0.0010975104            0    5269.5207     14.51057 
    1500    16738.481 -0.00057925965            0    5269.5211    14.510575 
    1550     16738.48            0            0    5269.5216    14.510582 
    1600     16738.48            0            0    5269.5216    14.510581 
    1650    16738.481            0            0    5269.5216    14.510581 
    1700    16738.481            0            0    5269.5217    14.510582 
    1750    16738.481            0            0    5269.5217    14.510583 
    1800    16738.481            0            0    5269.5217    14.510585 
    1850    16738.481            0            0    5269.5218    14.510585 
    1900    16738.481            0            0    5269.5218    14.510585 
    1950    16738.487 -0.0031700155            0    5269.5206    14.510534 
    2000    16738.514 -0.013238802            0    5269.5188    14.510401 
    2050    16738.578  -0.03654435            0    5269.5158    14.510155 
    2100    16738.656 -0.063182323            0    5269.5137    14.510082 
    2150     16738.63 -0.056004395            0    5269.5127    14.510096 
    2200    16738.579 -0.038415873            0    5269.5143    14.510273 
    2250    16738.538 -0.023709094            0     5269.516    14.510414 
    2300    16738.512 -0.013252539            0    5269.5182    14.510501 
    2350    16738.491 -0.0045593284            0    5269.5203    14.510598 
    2400    16738.482 -0.00052242487            0    5269.5217    14.510655 
    2450    16738.486 -0.0023245722            0    5269.5211    14.510627 
    2500    16738.491 -0.005189304            0    5269.5197    14.510606 
    2550    16738.604 -0.044988104            0    5269.5155    14.510185 
    2600    16738.446 0.0009675401            0    5269.5117    14.510521 
    2650    16732.887     1.753125            0    5269.5138    14.598792 
    2700    16738.784  -0.10629556            0    5269.5107    14.499176 
    2750    16734.136     1.359459            0    5269.5135    14.594678 
    2800    16738.608 -0.047184149            0    5269.5147    14.510254 
    2850    16738.509 -0.012527238            0    5269.5181    14.509344 
    2900    16738.487 -0.0026065529            0     5269.521    14.509512 
    2950    16738.498 -0.0082248532            0     5269.519    14.509457 
    3000    16738.683 -0.071294028            0     5269.514    14.509005 
    3050    16717.444    6.5874862            0    5269.4864    14.834144 
    3100    16657.654    25.431253            0    5269.5074    14.467824 
    3150    16739.322  -0.28964062            0     5269.497    13.658821 
    3200    16733.615    1.4969789            0     5269.487    11.998304 
    3250    16737.289   0.35071214            0    5269.4974    11.918931 
    3300    16732.493    1.8663821            0     5269.503    12.109003 
    3350    16738.717 -0.087719164            0    5269.5085    11.979747 
    3400    16738.586 -0.045267897            0    5269.5095     11.97972 
    3450    16738.662 -0.071274216            0    5269.5076    11.979564 
    3500    16738.853  -0.13644992            0    5269.5026    11.979658 
    3550    16729.612    2.7475277            0    5269.4774    12.195939 
    3600    16728.659     3.059607            0    5269.4893    12.241248 
    3650    16738.923  -0.15949792            0    5269.5014    11.991857 
    3700     16738.76  -0.10695054            0    5269.5028    11.992932 
    3750    16738.751  -0.10105954            0    5269.5057    11.993137 
    3800    16738.597 -0.048627545            0    5269.5097    11.993456 
    3850    16738.507 -0.016053927            0    5269.5138    11.992973 
    3900    16738.485 -0.0060825487            0    5269.5169    11.993052 
    3950    16738.475 -0.0014953722            0    5269.5183    11.993119 
    4000    16738.472 -0.00054315391            0    5269.5184     11.99315 
    4050    16738.472 -0.00023792126            0    5269.5187    11.993172 
    4100    16738.472            0            0    5269.5189    11.993188 
    4150    16738.472            0            0    5269.5189    11.993188 
    4200    16738.472            0            0     5269.519    11.993178 
    4250    16738.472            0            0     5269.519    11.993164 
    4300    16738.472            0            0    5269.5191    11.993152 
    4350    16738.473            0            0    5269.5191    11.993147 
    4400    16738.473            0            0    5269.5192    11.993149 
    4450    16738.473            0            0    5269.5192    11.993158 
    4500    16738.473            0            0    5269.5193     11.99317 
    4550    16738.473            0            0    5269.5193    11.993176 
    4600    16738.473            0            0    5269.5194    11.993174 
    4650    16738.473            0            0    5269.5194    11.993167 
    4700    16738.474            0            0    5269.5195    11.993162 
    4750    16738.474            0            0    5269.5195     11.99316 
    4800    16738.474            0            0    5269.5196     11.99316 
    4850    16738.474            0            0    5269.5196    11.993163 
    4900    16738.474            0            0    5269.5197     11.99317 
    4950    16738.474            0            0    5269.5197    11.993176 
    5000    16738.475            0            0    5269.5198    11.993174 
    5050    16738.475            0            0    5269.5198    11.993165 
    5100    16738.475            0            0    5269.5199    11.993155 
    5150    16738.475            0            0    5269.5199     11.99315 
    5200    16738.475            0            0      5269.52    11.993153 
    5250    16738.475            0            0      5269.52    11.993161 
    5300    16738.476            0            0    5269.5201    11.993173 
    5350    16738.476            0            0    5269.5201    11.993185 
    5400    16738.476            0            0    5269.5202    11.993189 
    5450    16738.476            0            0    5269.5202    11.993181 
    5500    16738.476            0            0    5269.5203    11.993165 
    5550    16738.483 -0.0030091905            0    5269.5195    11.993097 
    5600    16738.534 -0.020777802            0    5269.5177    11.992799 
    5650    16738.649 -0.059321662            0    5269.5153    11.993266 
    5700     16409.08    103.75288            0    5269.5745    23.626238 
    5750    16738.578 -0.036776519            0    5269.5155    11.910545 
    5800    16738.484 -0.0047306177            0     5269.518    11.911008 
    5850    16738.477 -0.00022082692            0    5269.5202    11.911078 
    5900    16738.477 -0.00033136078            0    5269.5203     11.91107 
    5950    16738.478 -0.00036902212            0    5269.5203    11.911052 
    6000    16738.477            0            0    5269.5206    11.911044 
    6050    16738.477            0            0    5269.5207    11.911034 
    6100    16738.478            0            0    5269.5207    11.911032 
    6150    16738.478            0            0    5269.5208    11.911037 
    6200    16738.478            0            0    5269.5208    11.911049 
    6250    16738.478            0            0    5269.5209    11.911062 
    6300    16738.478            0            0    5269.5209    11.911068 
    6350    16738.478            0            0     5269.521    11.911065 
    6400    16738.478            0            0     5269.521    11.911058 
    6450    16738.479            0            0    5269.5211    11.911052 
    6500    16738.479            0            0    5269.5211    11.911047 
    6550    16738.479            0            0    5269.5212    11.911046 
    6600    16738.479            0            0    5269.5212    11.911049 
    6650    16738.479            0            0    5269.5213    11.911056 
    6700    16738.479            0            0    5269.5213    11.911062 
    6750     16738.48            0            0    5269.5214     11.91106 
    6800     16738.48            0            0    5269.5214    11.911051 
    6850     16738.48            0            0    5269.5215    11.911044 
    6900     16738.48            0            0    5269.5215    11.911041 
    6950     16738.48            0            0    5269.5216    11.911045 
    7000     16738.48            0            0    5269.5216    11.911053 
    7050    16738.481            0            0    5269.5217    11.911063 
    7100    16738.481            0            0    5269.5217    11.911071 
    7150    16738.481            0            0    5269.5218    11.911072 
    7200    16738.481            0            0    5269.5218    11.911063 
    7250    16738.481            0            0    5269.5219    11.911048 
    7300    16738.481            0            0    5269.5219    11.911036 
    7350    16738.482            0            0     5269.522    11.911031 
    7400    16738.482            0            0     5269.522    11.911035 
    7450    16738.482            0            0    5269.5221    11.911046 
    7500    16738.482            0            0    5269.5221    11.911062 
    7550    16738.482            0            0    5269.5222    11.911077 
    7600    16738.482            0            0    5269.5222    11.911081 
    7650    16738.483            0            0    5269.5223    11.911071 
    7700    16738.483            0            0    5269.5223    11.911054 
    7750    16738.483            0            0    5269.5224    11.911039 
    7800    16738.483            0            0    5269.5224    11.911031 
    7850    16738.483            0            0    5269.5225    11.911031 
    7900    16738.483            0            0    5269.5226    11.911039 
    7950    16738.484            0            0    5269.5226    11.911052 
    8000    16738.484            0            0    5269.5227    11.911065 
    8050    16738.484            0            0    5269.5227     11.91107 
    8100    16738.484            0            0    5269.5228    11.911065 
    8150    16738.484            0            0    5269.5228    11.911056 
    8200    16738.484            0            0    5269.5229    11.911047 
    8250    16738.485            0            0    5269.5229    11.911042 
    8300    16738.485            0            0     5269.523    11.911041 
    8350    16738.485            0            0     5269.523    11.911046 
    8400    16738.485            0            0    5269.5231    11.911055 
    8450    16738.485            0            0    5269.5231    11.911062 
    8500    16738.485            0            0    5269.5232     11.91106 
    8550    16738.486            0            0    5269.5232    11.911053 
    8600    16738.487 -0.00084974055            0    5269.5227    11.911032 
    8650    16738.486            0            0    5269.5233    11.911046 
    8700    16738.486            0            0    5269.5234     11.91105 
    8750    16738.486            0            0    5269.5235    11.911056 
    8800    16738.486            0            0    5269.5235    11.911063 
    8850    16738.487 -0.000227631            0    5269.5234    11.911065 
    8900    16738.487            0            0    5269.5236    11.911068 
    8950    16738.487            0            0    5269.5237    11.911058 
    9000    16738.487            0            0    5269.5237    11.911045 
    9050    16738.487            0            0    5269.5238    11.911036 
    9100    16738.487            0            0    5269.5238    11.911034 
    9150    16738.488            0            0    5269.5239     11.91104 
    9200    16738.488            0            0    5269.5239    11.911052 
    9250    16738.488            0            0     5269.524    11.911068 
    9300    16738.488            0            0     5269.524    11.911079 
    9350    16738.488            0            0    5269.5241    11.911078 
    9400    16738.492 -0.0016306433            0    5269.5235    11.911038 
    9450    16738.492 -0.0032567425            0     5269.522    11.911005 
    9500    16738.495 -0.0036645345            0    5269.5224    11.910982 
    9550     16738.49 -0.001067391            0    5269.5237    11.911012 
    9600    16738.489            0            0    5269.5244    11.911032 
    9650    16738.489            0            0    5269.5244    11.911043 
    9700     16738.49            0            0    5269.5245    11.911058 
    9750     16738.49            0            0    5269.5245    11.911071 
    9800     16738.49            0            0    5269.5246    11.911073 
    9850     16738.49            0            0    5269.5246    11.911065 
    9900     16738.49            0            0    5269.5247    11.911053 
    9950    16738.491 -0.00058544648            0    5269.5243    11.911032 
   10000    16738.493 -0.0015244933            0    5269.5242    11.911015 
Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms

Performance: 36535.358 tau/day, 4228.629 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0030635  | 0.0035263  | 0.0040903  |   0.7 |  0.15
Neigh   | 0.0093439  | 0.01002    | 0.010976   |   0.6 |  0.42
Comm    | 0.11912    | 0.12509    | 0.13346    |   1.5 |  5.29
Output  | 0.003411   | 0.0038449  | 0.0050123  |   1.1 |  0.16
Modify  | 2.1961     | 2.2052     | 2.2137     |   0.5 | 93.25
Other   |            | 0.01717    |            |       |  0.73

Nlocal:          20.25 ave          27 max           9 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost:           31.5 ave          51 max          15 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:              1 ave           4 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 4
Ave neighs/atom = 0.049382716
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:02
